ANIHWA call2 - A bacteriophage-based approach to reducing infections caused by antibiotic resistant Escherichia coli

Antibiotic resistance is a significant and increasing problem in many types of bacteria which cause disease (pathogens) in animals and humans. Escherichia coli is among the most important of these pathogens, because of its role in intestinal, urinary tract and respiratory disease, and septicaemia in a variety of livestock species, including poultry; and also because many strains of E. coli that are associated with septicaemic infections in animals and humans are closely related. Antibiotic resistance in E. coli strains is increasing worldwide and this resistance can be maintained even after reducing or withdrawing antibiotic use. As such, the treatment of E. coli infections in animals and humans requires a new and sustainable approach. This project will investigate the use of bacteriophage as a biological control against harmful strains of E. coli which infect chickens. Bacteriophage, often contracted to 'phage', are viruses which infect and kill bacteria. They are quite specific, only affecting the targeted bacterial species while leaving other bacterial flora unharmed. Phages do not infect animals or humans and are widely distributed in the environment. As such, the use of phages to selectively kill harmful strains of E. coli which infect animals has the potential to be a natural and sustainable alternative to antibiotics, and may also result in new treatments for antibiotic resistant bacterial infections in humans. The effective application of phage therapy will require a thorough understanding of phage-bacteria interactions in a range of environments. This project will use laboratory experiments to build a comprehensive understanding of how phages infect E. coli strains under different environmental conditions. This information will then be used to design protocols for the optimal use of phage therapy to treat infections in animals.

The use of host-specific bacteriophage to target pathogenic strains of E. coli has the potential to be an effective and viable alternative to antimicrobial chemotherapy. The selection of suitable bacteriophage biocontrol candidates requires the in depth characterisation of the virus and detailed analysis of how phages interact with their hosts in vitro and in vivo. We will isolate phages from the environment, surface water, farms, drains and sewage which are able to infect a range of Avian Pathogenic Escherichia coli (APEC) serotypes. These will be characterised in vitro, and bacteriophage biocontrol candidates will be selected for evaluation in an E. coli septicaemia model in chickens. Selection of the phage will be based on the ability to infect a wide range of pathogenic E. coli strains, in vitro phage replication kinetics, and lack of/minimal host resistance. The potential issue of E. coli resistance to phage infection will be addressed by (i) targeting surface receptors which are important for virulence and/or antibiotic resistance, (ii) the use of cocktails of phages which target different receptors, and (iii) studying the CRISPR-Cas system of wild strains of E. coli to determine its role in phage resistance and its epidemiology and evolution during phage infection. This approach can synergise with the development of new drugs and has the potential to provide a sustainable platform for control of antibiotic-resistant pathogens which could easily be extrapolated to many other animal pathogens.

This proposal is in response to a BBSRC-supported research call from the Animal Health and Welfare (ANIHWA) ERA-Net to address antimicrobial and anthelmintic resistance by developing alternative curative and preventative therapies. There is general agreement that colibacillosis is the most common infectious bacterial disease of poultry and is responsible for significant economic loss worldwide. The major potential areas of impact are:
(i) The successful development of bacteriophage administration for APEC strains will reduce morbidity in infected chickens and reduce antibiotic usage, the economic scale of which is large but unquantifiable.
(ii) Successful commercial exploitation could result in widespread use off this approach with financial benefits.
(iii) Use of APEC infections represents a useful model for other bacterial pathogens where resistance is increasingly a problem, including the Pasteurella group of bacteria.
(iv) The use of phage therapy to control extraintestinal Escherichia coli (ExPEC) infections in birds is a useful comparative medicine model which may directly benefit human patients suffering from ExPEC infections such as meningitis, septicaemia and urinary tract infections.